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Yorodumi- PDB-1yon: Escherichia coli ketopantoate reductase in complex with 2-monopho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yon | ||||||
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Title | Escherichia coli ketopantoate reductase in complex with 2-monophosphoadenosine-5'-diphosphate | ||||||
Components | 2-dehydropantoate 2-reductase | ||||||
Keywords | OXIDOREDUCTASE / ketopantoate / NADP+ DEPENDENT / 2'-monophosphoadenosine-5'-diphosphate / pantothenate pathway / secondary alcohol dehydrogenase | ||||||
Function / homology | Function and homology information 2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ciulli, A. / Lobley, C.M.C. / Tuck, K.L. / Williams, G. / Smith, A.G. / Blundell, T.L. / Abell, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: pH-tuneable binding of 2'-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study. Authors: Ciulli, A. / Lobley, C.M. / Tuck, K.L. / Smith, A.G. / Blundell, T.L. / Abell, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yon.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yon.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/1yon ftp://data.pdbj.org/pub/pdb/validation_reports/yo/1yon | HTTPS FTP |
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-Related structure data
Related structure data | 1ks9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit comtains one functionally active monomer |
-Components
#1: Protein | Mass: 33907.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: panE / Plasmid: pET24b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A9J4, 2-dehydropantoate 2-reductase |
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#2: Chemical | ChemComp-A2R / [( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10% 2-methyl-2,4-pentanediol, 0.1M sodium acetate, 2mM NADPH, 2mM pantoate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2004 |
Radiation | Monochromator: SLIT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 29230 / Num. obs: 28985 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1760 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KS9 Resolution: 1.95→19.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.075 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.052 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.946→1.997 Å / Total num. of bins used: 20
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